Ecology of bacterial communities during petroleum biodegradation: a molecular analysis on degrading consortia isolated from hydrocarbon polluted soils, sediment and seawater samples

Environmental microbial communities are key players in the transformation and miner- alization of hydrocarbon pollutants. The aim of this study was to assess changes in bacterial abundance and diversity during the degradation of Tunisian Zarzatine oil by four indigenous bacterial consortia isolated from different polluted environmental matrix (a petroleum sta- tion soil, refinery reservoir soil, harbor sediment and harbor seawater). The microcosms were inoculated for two months with either a defined bacterial consortium and Zarzatine crude oil as only carbon and energy source. The microbial community dynamics was evaluated weekly in microcosms using Illumina 16S rRNA gene sequencing. An average of 7020 sequences per samples were obtained, the measured coverage was higher than 97% and more than 60% of sequence were correctly classified at species level. Degrading consortia enriched from soil and sediments were dominated by species belonging to Pseudomonas and Acinetobacter gen- era, while in the seawater-derived consortia Dietzia, Fusobacterium and Dicoplana emerged as dominant genera. We identified specific OTUs whose relative abundances bloomed from small to high percentages and were significantly correlated to total petroleum degradation: an OTU classified as Dietzia daqingensis in the seawater microcosms, and three OTUs classified as Acinetobacter venetianus in all two soils and sediment derived microcosms. Interestingly, a comparative analysis showed that this was the same OTU in all 3 microcosms which were derived from consortia isolated from different types (soil or sediment) and location. The work provides detailed insights about the modulation of bacterial communities involved in petroleum biodegradation.